CN114480734A - Specific primer for detecting passionflower latent virus and application thereof - Google Patents
Specific primer for detecting passionflower latent virus and application thereof Download PDFInfo
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- CN114480734A CN114480734A CN202210025079.8A CN202210025079A CN114480734A CN 114480734 A CN114480734 A CN 114480734A CN 202210025079 A CN202210025079 A CN 202210025079A CN 114480734 A CN114480734 A CN 114480734A
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- C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
- C12Q1/701—Specific hybridization probes
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/686—Polymerase chain reaction [PCR]
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
- C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
Abstract
The invention discloses a specific primer for detecting passion flower latent virus and application thereof. The nucleotide sequence of the specific primer is shown in a sequence table SEQ ID NO: 3 and SEQ ID NO: 4, respectively. The invention provides a primer pair for detecting passion fruit latent virus, which has universality, can be used for detecting passion fruit latent virus on different varieties of passion fruit, different passion fruit plants and exotic plants (such as persimmon), simultaneously establishes a molecular detection system of the passion fruit latent virus, enlarges the detection range of the passion fruit virus diseases, and simultaneously has important guiding significance for preventing and controlling the passion fruit virus disease detection and developing the virus molecular diagnosis technology.
Description
Technical Field
The invention belongs to the technical field of plant pathogen identification and disease control, and particularly relates to a specific primer for detecting passion flower latent virus on passion flower and a detection system thereof.
Background
Passiflora edulis is a Passiflora plant of Passiflora of Passifloraceae, also known as passion fruit and passion fruit, and is an important fruit for both food and medicine in tropical and subtropical regions. The southern areas of China such as Fujian, Guangxi, Guangdong and the like are cultivated. The main cultivated species include Huangguo Tainong No. 1, Huangjin fruit and Ziguo Zixiang No. 1, Mantianxing, etc.
Passiflora occulta latent virus (PLV) is a member of the genus Dianthus occulta (Carlavus), a linear, positive single-stranded RNA genome. The virus has been reported to infect Persimmon trees of the genus Diospyros (persimmons) and ornamental passion plants (Passiflora tarminiana), and there has been no report of infection with passion fruit (Passiflora edulis). In 2016-2019, a plant showing slight mottle symptom is found in the disease survey of mosaic disease on passion flower in southern areas of China, and serology and molecular biology detection exclude viruses of cucumovirus, potyvirus and geminivirus which can cause mosaic symptom.
The rapid detection of the virus diseases provides technical conditions for the prevention and control of the diseases, and the detection and identification of the virus pathogens on the passion flower mainly comprise the technologies of biological detection, electron microscopy, serological detection, molecular biological detection and the like at present. RT-PCR is an important molecular biological detection means, and is applied to detection and identification of a plurality of RNA viruses due to simple and convenient operation, high sensitivity and strong specificity.
The invention establishes an RT-PCR system for detecting passion fruit latent virus, provides technical support for obtaining the virus genome information and detection and identification, and has certain guiding significance for preventing and controlling passion fruit virus diseases.
Disclosure of Invention
The invention aims to provide a specific primer for detecting passion flower latent virus and application thereof.
BLAST compares PLV nucleotide sequences on all registered GeneBank, including PLV nucleotide sequences on Persimmon trees and ornamental passion plants, and designs specific detection primer pairs (Table 1) according to conserved segments of PLV coat protein (cp) sequences, wherein the primer pairs can be used for detection and identification of passion latent viruses on passion plants such as passion fruit (Passiflora edulis), dragon fruit (Passiflora foetida), passion flower (Passiflora tarninana) and Persimmon trees (persimmons).
A DNA fragment for detecting passion flower latent virus, wherein the sequence of the DNA fragment is shown in a sequence table SEQ ID NO: 1 or SEQ ID NO: 2, respectively.
A specific primer for detecting passion flower latent virus has a nucleotide sequence shown in a sequence table SEQ ID NO: 3 and SEQ ID NO: 4, respectively.
The kit comprises the specific primer for detecting the passion flower latent virus.
A detection method of passion flower latent virus adopts a PCR amplification method, and an amplification primer adopts a primer sequence shown in a sequence table SEQ ID NO: 3 and SEQ ID NO: 4, and (b) a primer pair shown in the specification;
the specific detection steps are as follows:
(1) collecting samples: samples of plants suspected of PLV infection were collected, marked and placed in a sealed bag and brought back to the laboratory as soon as possible.
(2) And (3) extracting total RNA, wherein the total RNA extraction is carried out according to the operation instruction of the total RNA extraction kit of the Tiangen polysaccharide polyphenol plant. The obtained plant total RNA is stored in a refrigerator at-80 ℃ for later use.
(3) The reverse transcription system is as follows: the following ingredients were added to a 1.5mL centrifuge tube:
2 μ g total RNA;
1 μ L of 6-base random primer (10 μ M);
denaturing at 70 deg.C for 5min, and standing on ice for 1 min;
5 μ L of 5 XM-MLV Buffer was added;
1 μ L dNTPs (10 mM); 0.6 μ L RNase inhibitor (50U/. mu.L);
1 μ L M-MLV reverse transcriptase (200U/. mu.L), complement ddH2O to 25 μ L.
After the reaction was terminated in a 37 ℃ water bath for 1 hour, the cDNA was stored at-20 ℃.
(4) The PCR reaction system is 25 mu L, cDNA obtained by reverse transcription is taken as a template, and the following components are added into a PCR tube:
2.5μL 10×Taq buffer;
1μL 10mM dNTPs;
1 μ L of forward primer PLV-1F (20 μ M);
1 μ L of reverse primer PLV-1R (20 μ M);
3μL cDNA;
0.15 μ L Taq DNA polymerase (5U/. mu.L)
The total volume was 25. mu.L. In the negative control system, ddH2O was used in place of the cDNA template.
The reaction conditions are as follows: 3min at 95 ℃; 30 cycles of 95 ℃ for 30s, 57 ℃ for 30s and 68 ℃ for 1 min; prolonging at 68 deg.C for 10 min;
(5) and (3) detecting the PCR product through 1.5% agarose gel electrophoresis, if the amplification product is 837bp, recovering and purifying the positive PCR product according to the specification of the Tiangen DNA gel cutting recovery kit, sequencing the obtained product by Huada Gene science and technology Limited, and performing BLAST analysis on the obtained sequence and a known sequence in GenBank to determine PLV infection.
The invention has the beneficial effects that: the invention provides a primer for specifically detecting PLV, the pair of primers has universality, and not only can detect PLV on main cultivars of passion fruit (such as Tainong No. 1, babysbreath and the like), but also can be used for detecting and identifying PLV on ornamental passion fruit, such as passion fruit, passion flower and the like, and persimmon trees. An RT-PCR detection system for specifically detecting PLV on passion flower is established for the first time in China, and the detection system has the advantages of simplicity and convenience in operation, strong specificity, high sensitivity and the like. Experiments show that the invention can be used for rapidly detecting the infection of PLV on passion flower and dragon fruit. The invention can be used for rapid detection and identification of PLV, expands the detection range of virus diseases of passion flower, and meets the disease detection requirements in agricultural production.
Drawings
FIG. 1 shows the symptoms exhibited by PLV on passion flower (normal leaves on the left and infected leaves with PLV on the right).
FIG. 2 is a gel electrophoresis image of PLV on 5 total samples of passion flower (Tainong No. 1) detected by RT-PCR. (Marker: DL2000, lanes 1-5 are disease samples numbered 2, 2g, 2k, 17, and lanes 6-7 are healthy and water controls, respectively).
FIG. 3 is a gel electrophoresis image of PLV on dragon fruit detected by RT-PCR method. (Marker: DL2000, lanes 1-4 are disease samples, lanes 5-6 are healthy and water controls).
Detailed Description
In order that the invention may be more fully understood, reference will now be made to the following description. This invention may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete.
Example 1: identification of unknown pathogen in passion flower (variety Tainong No. 1) in Fujian region
In 2016-2019, when the inventor conducts disease investigation on passion flower mosaic disease in southern China, the inventor finds that a sample (shown in figure 1) showing slight mosaic mottle has no positive reaction by using virus specific primers (such as cucumovirus, potato virus, tobamovirus and geminivirus) which are reported to cause the passion flower mosaic disease in China. Indicating the possible presence of new viral pathogens.
(1) Primer design
According to the PLV nucleotide sequence which is known to infect persimmon trees and passion flower of banana, the specific primers for RT-PCR detection of PLV are designed and synthesized according to the conserved sequence of the cp gene as follows:
(2) extraction of Total RNA
And (3) extracting total RNA, wherein the total RNA extraction is carried out according to the operation instruction of the total RNA extraction kit of the Tiangen polysaccharide polyphenol plant. The obtained plant total RNA is stored in a refrigerator at-80 ℃ for later use.
(3) The reverse transcription system is as follows: the following ingredients were added to a 1.5mL centrifuge tube:
2 μ g total RNA;
1. mu.L of 6-base random primer (10. mu.M);
denaturing at 70 deg.C for 5min, and standing on ice for 1 min;
5 μ L of 5 XM-MLV Buffer was added;
1 μ L dNTPs (10 mM); 0.6 μ L RNase inhibitor (50U/. mu.L);
1 μ L M-MLV reverse transcriptase (200U/. mu.L), complement ddH2O to 25. mu.L.
After the reaction was terminated in a 37 ℃ water bath for 1 hour, the cDNA was stored at-20 ℃.
(4) The PCR reaction system is 25 mu L, cDNA obtained by reverse transcription is taken as a template, and the following components are added into a PCR tube:
2.5μL 10×Taq buffer;
1μL 10mM dNTPs;
1 μ L of forward primer PLV-1F (20 μ M);
1 μ L of reverse primer PLV-1R (20 μ M);
3μL cDNA;
0.15 μ L Taq DNA polymerase (5U/. mu.L)
The total volume was 25. mu.L. In the negative control system, ddH2O was used in place of the cDNA template.
The reaction conditions are as follows: 3min at 95 ℃; 30 cycles of 95 ℃ for 30s, 57 ℃ for 30s and 68 ℃ for 1 min; prolonging at 68 deg.C for 10 min;
(5) the PCR product was detected by 1.5% agarose gel electrophoresis, and the amplification product was about 800-900bp, which was identical in size to the target sequence (FIG. 2). The PCR product is recovered, purified and sequenced, the sequence length is 837bp, and the obtained sequence is subjected to BLAST analysis with the known PLV sequence in GenBank to determine PLV infection (xfl-tn-5, the sequence is shown as the sequence table SEQ ID NO: 1).
Example 2: detection of PLV on strobilus
In order to further verify the universality of the primers in the invention, samples of suspected PLV-infected strobilus seu strobilus Pini are collected, and the primers in the invention are used for detecting 4 samples to be detected.
The specific detection steps are as follows:
(1) extracting total RNA: the total RNA extraction is carried out according to the operation instruction of the total RNA extraction kit of the Tiangen polysaccharide polyphenol plant. The obtained plant total RNA is stored in a refrigerator at-80 ℃ for later use.
(2) The reverse transcription system is as follows: the following ingredients were added to a 1.5mL centrifuge tube:
2 μ g total RNA;
1 μ L of 6-base random primer (10 μ M);
denaturing at 70 deg.C for 5min, and standing on ice for 1 min;
adding 5 mu L of 5 XM-MLV Buffer;
1 μ L dNTPs (10 mM); 0.6 μ L RNase inhibitor (50U/. mu.L);
1 μ L M-MLV reverse transcriptase (200U/. mu.L), complement ddH2O to 25 μ L.
After the reaction was terminated in a 37 ℃ water bath for 1 hour, the cDNA was stored at-20 ℃.
(3) The PCR reaction system is 25 mu L, cDNA obtained by reverse transcription is taken as a template, and the following components are added into a PCR tube:
2.5μL 10×Taq buffer;
1μL 10mM dNTPs;
1 μ L of forward primer PLV-1F (20 μ M);
1 μ L of reverse primer PLV-1R (20 μ M);
3μL cDNA;
0.15 μ L Taq DNA polymerase (5U/. mu.L)
The total volume was 25. mu.L. In the negative control system, ddH2O was used in place of the cDNA template.
The reaction conditions are as follows: 3min at 95 ℃; 30 cycles of 95 ℃ for 30s, 57 ℃ for 30s and 68 ℃ for 1 min; prolonging at 68 deg.C for 10 min;
(4) and (3) product verification: the PCR product is detected by 1.5% agarose gel electrophoresis, 1 amplified target band appears (figure 3), the positive PCR product is recovered and purified according to the specification of a Tiangen DNA gel cutting recovery kit, the obtained product is sent to Huada science and technology limited for sequencing, the obtained sequence and the known sequence in GenBank are subjected to BLAST analysis, and the infection of PLV is determined (lzg-1, the sequence is shown as SEQ ID NO: 2 in the sequence table).
The above-mentioned embodiments only express several embodiments of the present invention, and the description thereof is more specific and detailed, but not construed as limiting the scope of the invention. It should be noted that, for a person skilled in the art, several variations and modifications can be made without departing from the inventive concept, which falls within the scope of the present invention. Therefore, the protection scope of the present patent shall be subject to the appended claims.
Sequence listing
<110> research institute for subtropical plants in Fujian province
<120> specific primer for detecting passion flower latent virus and application thereof
<160> 4
<170> SIPOSequenceListing 1.0
<210> 1
<211> 836
<212> DNA
<213> carnation latent virus (Carlavus)
<400> 1
accaaaggaa gcaccagaag tggtcccgcc gccggttctc caccattgcc aatgaaagaa 60
aaggaggctt caagttcttc tgagccaaat gatgaggaat tacgccagcg aagattactg 120
aagttaattg aaatcctgca ggctcagaat cacaattcaa accttaagaa cgtgtccttc 180
gaaattggta ggccttctct tgagcgaccc cccgcaatgc gtagggaccc tgggaatcca 240
tatggaaggt tctccattga tgagcttttc aaaatgaagg tcgatctggt gtcgaataac 300
atggctacta cggagcagat ggcaaatatt atggcagata tagcgggcct tggtgtgccc 360
accgaacatg ttacctcctg tatactcaag atggtcatca tgtgcgctag tgttagtagt 420
tctgcctatc tggacccgga tggaagcgta gagtttgagg gtggtgcagt gccagttgat 480
tcaatagctg ctatcatgaa aaagcattca acgttaagga aagtatgcag gctgtacgct 540
ccgctggttt ggaacagcat gctagtgcgg aaccagccgc catctgattg gcaagctatg 600
ggtttccctt acaatgcgag gttcgcagct tttgacacct tcgattatgt gaccaacacc 660
gcggctatcc aaccagtcga aggtataatc aggagaccta ccgcagagga agtgatagcc 720
cacaatgccc acaaacgcct agctttggac aggtcgaata gaaatgagaa attcggcaat 780
ttggaaacag agtacactgg tggcttgcaa ggcgcagaaa tagtccgcaa tcatcg 836
<210> 2
<211> 837
<212> DNA
<213> carnation latent virus (Carlavus)
<400> 2
accaaaggaa gcaccagaag tgatcccgcc gccgattcct ccaccattgc caatgaagga 60
aaaggaggtc tcaagttctt ctgagccaaa tgatgaggaa ttacgccagc gaagattact 120
gaagttaatt gaaatcctgc aggctcagaa tcacaattca aaccttaaga atgtgtcctt 180
cgaaattggt aggccttctc ttgagcgacc ccccgcaatg cgtagggacc ctgggaatcc 240
atatggaagg ttctccattg atgagctttt caaaatgaag gtcgatctgg tatcgaataa 300
catggctact acggagcaga tggcaaatat catggcagat atagcgggtc ttggtgtgcc 360
cactgaacat gtcacctcct gtatactcaa gatggttatc atgtgcgcta gtgttagtag 420
ctccgcctat ctggatccgg atggaagcgt agagtttgag ggtggtgcag tgccagttga 480
ttcaatagcc gccatcatga agaagcattc aacgttaagg aaagtatgca ggttgtacgc 540
tccgctggtt tggaacagca tgctagtgcg gaaccagccg ccatctgact ggcaagctat 600
gggtttccct tacaatgcga ggttcgcagc ttttgacacc ttcgattatg tgaccaacac 660
cgcggctatc caaccagtcg aaggtataat caggagacct accgcagaag aagtgatagc 720
ccacaatgcc cacaaacgcc tagctttgga caggtcgaat agaaatgaga aattcggcaa 780
tttggaaaca gagtacactg gtggcttgca aggcgcagaa atagtccgca atcatcg 837
<210> 3
<211> 23
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<400> 3
gctgctacca atttcgacgg tca 23
<210> 4
<211> 21
<212> DNA
<213> Artificial Sequence (Artificial Sequence)
<400> 4
gcacccaaaa gtcccaagca c 21
Claims (4)
1. A DNA fragment for detecting passion flower latent virus, which is characterized in that the sequence of the DNA fragment is shown in a sequence table SEQ ID NO: 1 or SEQ ID NO: 2, respectively.
2. A specific primer for detecting passion flower latent virus is characterized in that the nucleotide sequence is shown in a sequence table SEQ ID NO: 3 and SEQ ID NO: 4, respectively.
3. A kit comprising the specific primers for detecting passion flower latent virus of claim 2.
4. A detection method of passion flower latent virus is characterized in that a PCR amplification method is adopted, and an amplification primer adopts a primer sequence shown in a sequence table SEQ ID NO: 3 and SEQ ID NO: 4, and (b) a primer pair shown in the specification;
3min at 95 ℃; 30 cycles of 95 ℃ for 30s, 57 ℃ for 30s and 68 ℃ for 1 min; prolonging at 68 deg.C for 10 min;
detecting the amplified product by 1.5 percent agarose gel electrophoresis, and sequencing, wherein if the amplified product is a sample of 837bp, the passion flower latent virus is obtained.
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Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2007033436A1 (en) * | 2005-09-26 | 2007-03-29 | The University Of Queensland | Modulation of gene expression and agents useful for same |
CN111424118A (en) * | 2020-04-24 | 2020-07-17 | 云南省农业科学院生物技术与种质资源研究所 | Multiplex composite PCR detection method for passionflower virus pathogen |
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2022
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Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO2007033436A1 (en) * | 2005-09-26 | 2007-03-29 | The University Of Queensland | Modulation of gene expression and agents useful for same |
CN111424118A (en) * | 2020-04-24 | 2020-07-17 | 云南省农业科学院生物技术与种质资源研究所 | Multiplex composite PCR detection method for passionflower virus pathogen |
Non-Patent Citations (6)
Title |
---|
J TANG ET AL.: "First Report of Passiflora latent virus in Banana Passionfruit (Passiflora tarminiana) in New Zealand", 《PLANT DIS.》 * |
S. SPIEGEL ET AL.: "The complete nucleotide sequence of Passiflora latent virus", 《ARCHIVES OF VIROLOGY》 * |
SPIEGEL,S. ET AL.: "Passiflora latent carlavirus, complete genome,ACCESSION DQ455582", 《GENBANK》 * |
TATSUSHI OGATA ET AL.: "In Vivo Micrografting to Eliminate Passiflora Latent Virus from Infected Passion Fruit Plants", 《THE HORTICULTURE JOURNAL》 * |
刘升学 等: "新疆啤酒花潜隐病毒的检测及外壳蛋白基因的序列分析", 《植物病理学报》 * |
陈媚 等: "西番莲病毒病研究进展", 《中国南方果树》 * |
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